As far as I know, while you can set the transparency for the polygon map as a whole, clicking on a polygon will indeed turn it into a solid color. I've found similar posts to the community but they are from a few years ago. This might be worth posting in Ideas !
If someone else knows otherwise, I'd love to know as well.
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I haven't tested this with polygon maps but I assume it should work the same way as other chart types. You can downgrade the transparency of the entire map and then instead of clicking on different stages on the map, you can click on the color legend of those stages, that should retain the color of your selection and transparency intensity and not look overpowering.
For any chart type, selecting something will actually 'select' that part of the chart making it more overpowering than the unselected parts. Clicking on the legend will not. So
this: clicking on a legend
versus this: selecting an area of the chart
will provide different results.
Hope that helps!